It's funny, but I just read an old thread from a couple years back on this same topic.
Of the games I've played...
Thief Dark Shadows-- The Shalebridge Cradle level. A masterpiece. How many years has it been since I played this? I remember every detail. Perfect design. Not worried about spoilers anymore, so I'll add that the entire first half of the mission was free of ANY enemies. But you don't know that. The designers masterfully used lighting and soundscape to twist your brain in knots. I did a quick search just now to see if anyone has ever written a tribute piece and found
this from Polygon . One of the greatest levels in gaming for me.
And
here is another piece written about this level. This one goes in to a great amount of depth. Very interesting if you recall this mission.
Thief Dark Project -- The Cathedral gave me the chills. This time you could see ghosts, but again, the sound design was amazing and made it quite scary for me. Hair raising
F.E.A.R -- Creepy little girls are uber frightening!
Subnautica -- A combination of depth, darkness and yep, sound design made some parts of Subnautica scary indeed.
Stalker -- Many of the underground levels were scary, at least the first time. Who wasn't frightened the first time a burer picked up a crate and telepathically hurled it at you while you had no idea what just did that?
Headcrabs -- To this day they are still the source of 90% of all jump scares in my gaming history. I bought Black Mesa just yesterday and they have lost that novelty. But back in the day? Always when least expected!
I've avoided games like Resident Evil and Silent Hill. Never played Alien Isolation. I bought Outcast years ago and don't play it. Darkwood too. I know those games will scare me